Biology subjects

Ramakrishnan, U.

Publications and source records attributed to Ramakrishnan, U..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Extreme in Every Way: Exceedingly Low Genetic Diversity in Snow Leopards Due to Persistently Small Population Size

Snow leopards (Panthera uncia) serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous Anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. They are the least studied genetically of all big cat species with more to learn regarding their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer new insights into these unresolved questions. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin, as previously identified, and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest genetic diversity of any big cat species, due to a persistently small population size (relative to other big cat species) throughout their evolutionary history rather than recent inbreeding. Without a large population size or ample standing genetic variation to help buffer them from any forthcoming Anthropogenic challenges, snow leopard persistence may be more tenuous than currently appreciated.

evolutionary biology↗

bioRxiv2023

On the road to losing connectivity: Fecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India

Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data is required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used fecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single nucleotide polymorphism (SNP) data for 124 Gaur and 99 Sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred-Karhandala Wildlife Sanctuary. Although Sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although landcover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species, respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.

genomics↗

bioRxiv2023

Host-pathogen-vector continuum in a changing landscape: Drivers of Bartonella prevalence and evidence of historic spillover in a tropical multi-host community

Small mammals and their ectoparasites present a unique system to investigate the eco-epidemiology of multi-host vector-borne pathogens and identify specific bacterial spillover determinants. We applied ecological and evolutionary analyses in a rainforest-human-use mosaic to investigate Bartonella spp. across small mammal and ectoparasite communities. We observed substantial overlap among small mammal communities in different habitat types, predominantly driven by habitat generalists. Most ectoparasites were generalists, infecting multiple hosts. We observed high Bartonella prevalence at both study sites -a forest-plantation mosaic (47.4%) and a protected area (28.8%). Seven of the ten ectoparasite species sampled were also positive for Bartonella, following prevalence trends in their hosts. A generalised linear model revealed an independent association between aggregated ectoparasite load in hosts and Bartonella prevalence, implicating ectoparasites in transmission. Bartonella lineages from small mammals were host-specific, while ectoparasites carried Bartonella associated with other small mammal hosts, indicating the potential for cross-species transmission. Phylogenetic ancestral trait reconstruction of Bartonella haplotypes suggest historic spillover events in the small mammal community, validating the potential for contemporary spillover events. These results highlight the necessity to disentangle the complex relationship between hosts, ectoparasites, and pathogens to understand the zoonotic implications of undetected spillover events in such multi-host communities.

ecology↗

bioRxiv2023

Serial dilution shapes genetic variation and defines conservation units in Asian elephants

Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analysed 34 whole genomes (between 11X - 32X) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern) India, Central India and three in Southern India. Our genetic data reveal signatures of serial colonisation, and a dilution of genetic diversity from north to south of India. The Northern populations diverged from other populations more than 70,000 years ago, have higher genetic diversity, and low inbreeding/high effective size (Pi = 0.0016{+/-}0.0001; FROH> 1MB= 0.09{+/-}0.03). Two of three populations in Southern India (South of Palghat Gap: SPG, and South of Shencottah Gap:SSG) have low diversity and are inbred, with very low effective population sizes compared to current census sizes (Pi = 0.0014{+/-}0.00009 and 0.0015{+/-}0.0001; FROH> 1MB= 0.25{+/-}0.09 and 0.17{+/-}0.02). Analyses of genetic load reveals purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the Southern populations and potential dilution of all deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity make these populations (SPG and SSG) high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to geographic signatures of serial founding events, even in large, highly mobile, endangered mammals.

evolutionary biology↗

bioRxiv2023

Spatial patterns in the diet of Gyps vultures in India and their implications for conservation

Dietary analyses are particularly useful for developing conservation programmes for species threatened by resource depletion, poisoning and environmental pollution. Gyps vultures in South Asia represent one such case, having undergone a population collapse caused by feeding on carcasses of cattle treated with the non-steroidal anti-inflammatory drug diclofenac. Following a ban on the veterinary use of diclofenac, populations of vultures remain low and mostly concentrated near protected areas. Understanding the role of protected areas in the recovery of these critically endangered species requires analyses of spatial variation in their diet. We used faecal metabarcoding to investigate the spatial variation in the diet of Gyps vultures across four landscapes from sites located inside and outside protected areas. We collected faecal 642 samples, of which 419 yielded adequate molecular data to identify the vulture species and 30 molecular operational taxonomic units corresponding to at least 28 diet species. The diet was dominated by large ungulates and varied across landscapes, protection status and vulture species, with the observed variation largely explained by differential intake of wild and domestic species. Domestic livestock was present in >95% of the samples from central, west and north India, but 77% of the samples had only wild species in south India. This variation was explained by livestock density within 100 km radius of the sampling site. Our results imply that protected areas may not offer a respite from possibility of diclofenac-poisoning across most parts of the country and efforts should continue unabated to remove nephrotoxic drugs from veterinary use.

ecology↗

bioRxiv2023

Unraveling the Genomic Diversity and Evolutionary History of Captive Tigers in the United States

Genomic studies of rare and endangered species have focused broadly on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated the genomic diversity potentially housed in captive populations. For tigers (Panthera tigris) in particular, captive individuals vastly outnumber those in the wild, yet the diversity of the captive population remains largely unexplored. Here, we present the first large-scale genetic study of the private (non-zoo) captive tiger population in the United States (U.S.), also known as Generic tigers. We find that the U.S. Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies (P. t. altaica, Amur; P. t. tigris, Bengal; P. t. corbetti, Indochinese; P. t. jacksoni, Malayan; P. t. amoyensis, South China; P. t. sumatrae, Sumatran). We show that the Generic tiger population has a comparable amount of genetic diversity to most wild subspecies, relatively few private variants, and fewer deleterious mutations. We also observe inbreeding coefficients that are similar to wild populations, suggesting that inbreeding in captive populations is not pervasive, although there are some individuals within the Generic population that are substantially inbred. Our results elucidate the admixture history of the Generic tiger population in the U.S. Additionally, we develop a reference panel for tigers and show that it can be used with imputation to accurately distinguish individuals and assign ancestry even with ultra-low coverage (0.25x) data. The study and reference panel will provide a resource to assist in tiger conservation efforts.

evolutionary biology↗

bioRxiv2023

Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru

Genomic surveillance in response to coronavirus disease (COVID-19) pandemic is crucial for tracking spread, identify variants of concern (VoCs) and understand the evolution of its etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). India has experienced three waves of COVID-19 cases, which includes a deadly wave of COVID-19 that was driven by the Delta lineages (second/Delta wave) followed by another wave driven by the Omicron lineages (third/Omicron wave). These waves were particularly dramatic in the metropolitan cities due to high population density. We evaluated the prevalence, and mutational spectrum of SARS-CoV-2 variants/lineages in one such megapolis, Bengaluru city, across these three waves between October 2020 and June 2022. 15,134 SARS-CoV-2 samples were subjected to whole genome sequencing (WGS). Phylogenetic analysis revealed, SARS-CoV-2 variants in Bengaluru city belonged to 18 clades and 196 distinct lineages. As expected, the Delta lineages were the most dominant lineages during the second wave of COVID-19. The Omicron lineage BA.2 and its sublineages accounted for most of the COVID-19 cases in the third wave. Most number of amino acid changes were observed in spike protein. Among the 18 clades, majority of the mutations and least similarity at nucleotide sequence level with the reference genome were observed in Omicron clades.

genomics↗

bioRxiv2022

Genomic Variation, Population Structure, and Gene Flow across Asian Pikas

Asian pikas have one of the most complex systematics and evolutionary history. The Himalayas is an important habitat for Asian pikas as it hosts 23 - 25% of pikas global diversity and has provided the ancestral training ground for local adaptation to high altitudes. They are one of the most abundant species in the Himalayas and Qinghai Tibetan Plateau (QTP), however genetic studies to explore their population structure and evolution are limited. Here, we utilize a population genomics approach using ~28,000 genome-wide SNP markers obtained from restriction-site associated DNA sequencing in six species of Asian Pikas (Ochotona spp.) that are distributed across the Himalayas and neighboring high-altitude mountains. We examined intra- and inter-species genetic diversity, population structure, phylogenetic history and explored processes that shaped the current genetic diversity of Pikas across the Himalayas. We identified low nucleotide diversity and high inbreeding coefficient across all species which possibly indicated decreasing population size in these species. We also identified extensive evidence of gene flow (both historic and contemporary) across these species. Our findings indicate that inter-species gene flow is a key evolutionary process that has been countering the negative effect of low genetic diversity among Asian pikas.

evolutionary biology↗

bioRxiv2022

Prioritizing landscapes to reconcile biodiversity conservation, ecosystem services, and human well-being in India

Biodiversity conservation and human well-being are tightly interlinked; yet mismatches in the scale at which both priorities are planned and implemented have exacerbated biodiversity loss, erosion of ecosystem services, and declining human quality of life. India houses the second largest human population on the planet, while <5% of the countrys land area is effectively protected for conservation. This warrants landscape-level conservation planning through a judicious mix of land-sharing and land-sparing approaches, and co-production of ecosystem services. Through a multi-faceted assessment, we prioritize spatial extents of land parcels that, in the face of anthropogenic threats, can safeguard conservation landscapes across Indias biogeographic zones. We find that only a fraction (~15%) of such priority areas identified here are encompassed under Indias extant PA network, and several landscapes of high importance were omitted in all previous global-scale assessments. We then examined the spatial congruence of priority areas with administrative units earmarked for economic development by the Indian government, and propose management-zoning through state-driven and participatory approaches. Our spatially explicit insights can help meet the twin goals of biodiversity conservation and sustainable development in India and other countries across the Global South.

ecology↗

bioRxiv2022

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of their genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140{square}Mb, with 19{square}scaffolds, corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies which will improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 tRNAs and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to tigers apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of non-invasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.

genomics↗

bioRxiv2021

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole genomes sequencing from 57 tigers to estimate individual inbreeding and mutation loads in a small-isolated, and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH=0.57) than the large-connected (FROH=0.35 and FROH=0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at high frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of (a) high mutation load; (b) purging and (c) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation should offset any possible impacts of inbreeding depression. Significance statementHabitat fragmentation is sequestering species into small and isolated populations with high chances of extinction. But are small and isolated populations at risk of extinction from inbreeding depression, or does inbreeding and purging of deleterious alleles reduce such threat? Using whole genomes from several wild Indian tiger populations, we provide evidence supporting purging of highly deleterious variants in a small isolated population. However, our analyses also indicate that the remaining highly deleterious alleles are at high frequencies, suggesting continued inbreeding depression despite some successful purging. We discuss the implications of our results for conservation, including possible genomics-informed genetic rescue strategies.

evolutionary biology↗

bioRxiv2019

Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures

An understanding of the factors affecting the diet composition of critically endangered Gyps vultures in the Indian subcontinent has important applications to the design of effective conservation strategies. After suffering a massive decline (~99%) in numbers caused by veterinary use of the nephrotoxic drug diclofenac, vultures now persist in very low numbers, mostly concentrated within or near National Parks. This spatial association might be attributed to the availability of wild ungulate carcasses free from toxic veterinary drugs. Hence, quantification of vulture diets and the factors affecting them is critical to test this hypothesis. Here, we describe and validate a robust \"field-to-benchtop-to-desktop\" metabarcoding workflow for assessing the species- and sex-specific diet of these obligate scavengers from non-invasively collected faecal samples. Seven metabarcodes targeting mitochondrial and nuclear genes were used to simultaneously determine the vulture species identity, sex and species consumed. The amplicons were sequenced using an Illumina Miseq platform. We included controls and three replicates per sample to establish a series of non-arbitrary thresholds to filter the sequence data and eliminate cross-contamination, PCR/sequencing errors and false positives. Using this strategy enabled identification of species and sex for all samples. Diet species-specific sequences could be identified with high taxonomic resolution for 93% of samples. Out of the seven metabarcodes, just four were sufficient to meet the objectives. From this preliminary analysis, domestic livestock seem to be the most frequently consumed diet item across samples from inside and outside protected habitats. Our method provides a rapid and reliable tool for describing large-scale variation in consumption of domestic versus wild species in the diet of these species, paving the way for a better understanding of the role protected areas play in persistence and recovery of the remaining Gyps vulture populations in the wild.

genetics↗

bioRxiv2019

Is shed hair the most effective non-invasive resource for estimating wild pedigrees?

Wild pedigrees are critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, many identified individuals will have to be genotyped at thousands of loci, mostly from non-invasive samples. This requires us to quantify (a) the most common non-invasive sample available from identified individuals (b) the ability to acquire genome-wide data from such samples, and (c) the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population. We followed identified individuals from a wild endangered tiger population, and found that shed hair samples were most common compared to fecal samples, carcasses and opportunistic invasive samples. DNA extraction, library preparation and whole genome sequencing resulted in between 126,129 and 512,689 SNPs from across the genome for four such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases, and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages as suggested by long-term monitoring data. Even with these few samples, we were able to uncover the matrilineage for an individual with unknown ancestry. In summary, we demonstrated that non-invasive shed hair samples yielded adequate quality/quantity DNA AND in conjunction with sensitive library preparation methods, provided reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair are an effective resource for studying individual-based genetics of elusive endangered species.

genomics↗

bioRxiv2019

Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape

AimMaintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on connectivity in four wide-spread species- jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris). Location Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land-use types.\n\nMethodsMicrosatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on gene flow was inferred using a multi-model landscape resistance optimization approach.\n\nResultsAll four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on geneflow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables- land-use, human population density, density of linear features and roads- impacted the study species differently. Although land-use was found to be an important variable explaining genetic connectivity for all four species, the amount of variation explained, the optimum spatial resolution and the resistance offered by different land-use classes varied.\n\nMain conclusionsAs expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.

ecology↗

bioRxiv2019

Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection

Formulating strategies for species conservation requires knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, the evolutionary history and genomic variation of tigers remain poorly known. With 70% of the worlds wild tigers living in India, such knowledge is critical for tiger conservation. We re-sequenced 65 individual tiger genomes across their extant geographic range, representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding, possibly because of small and fragmented protected areas. Surprisingly, demographic models suggest recent divergence (within the last 10,000 years) between populations, and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection mainly related to metabolic adaptation to cold, while Sumatran tigers show evidence of evolving under weak selection for genes involved in body size regulation. Depending on conservation objectives, our results support the isolation of Amur and Sumatran tigers, while geneflow between Malayan and South Asian tigers may be considered. Further, the impacts of ongoing connectivity loss on the health and persistence of tigers in India should be closely monitored.

genomics↗

bioRxiv2019

Reconsidering the management paradigm of fragmented populations

Habitat fragmentation and population declines call for informed management of many endangered species. The dominant paradigm for such management focuses on avoiding deleterious inbreeding effects in separated populations, by facilitating migration to maintain connectivity between them, an approach epitomized by the \"one migrant per generation\" rule. We show that this paradigm fails to take into account two important factors. First, it ignores an inherent trade-off: maintaining within-population genetic diversity is at the expense of maintaining global diversity. Migration increases local within-population genetic diversity, but also homogenizes the meta-population, which may lead to erosion of global genetic diversity. Second, this paradigm does not consider that because many fragmented species have declined in numbers only within the last century, they still carry much of the high genetic diversity characteristic of the historically large population. The conservation of a species global diversity, crucial for evolutionarily adaptation to ecological challenges such as epidemics, industrial pollutants, or climate change, is paramount to a species long-term survival. Here we discuss how consideration of these factors can inform management of fragmented populations and provide a framework to assess the impact on genetic diversity of different management strategies. We also propose two alternative management strategies to replace the \"one migrant per generation\" dogma.

ecology↗

bioRxiv2018

Empowering conservation practice with efficient and economical genotyping from poor quality samples

O_LIModerate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations. C_LIO_LIHowever, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from labor medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites. C_LIO_LITo enable genotyping in conservation contexts, we used next-generation sequencing of multiplex PCR products from very low-quality DNA extracted from feces, hair, and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch. C_LIO_LIWe genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives, and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog/Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure. C_LIO_LIWe provide proof-of-concept for a rapid, simple, cost-effective, and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade. C_LI

genomics↗

bioRxiv2017

Coalescent theory of migration network motifs

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a large mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with small density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into several disconnected components. We illustrate our results using two example datasets--sky island birds of genus Brachypteryx and Indian tigers--identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity and for designing strategies to alter population migration networks to maximize genetic variation in the context of conservation of endangered species.

genetics↗